.MRXS files in ICY

[hen...@broadpark.no]

Hi, anyone know a way to import .MRXS image files to ICY? I tried but got "image plane too large". 

thanks

[Stephane]

Hello,

Sorry for the delay !
Actually mirax format is not yet supported by Bio-Formats (the library we use to open image files) :

http://www.openmicroscopy.org/site/support/bio-formats/supported-formats.html
http://trac.openmicroscopy.org.uk/ome/ticket/4121

But at some point they will add support for it.
From the error message we counld think your image is too big to be laoded, do you know the size (X / Y dimension) of your image ?

- Stephane

[Henrik Aamodt]

hi, thanks for Your reply. we will be able to scan to .tiff soon, that should resolve the issue. FYI the mirax files are aprox 4.5-5 GB, dont have the x/y

henrik aamodt

norway

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[Stephane]

Hi,

4 or 5 GB is really huge image, if the X/Y dimension is too large (> 32000x32000) then you may experience problems to open them.

[henrik aamodt]

Hi again, thank You for Your reply. Is there a quick way to reduce the X/Y in images, or has that to be done before importing them to ICY or maybe even when the slides are beeing scanned?

sincerly
Henrik Aamodt
Oslo University Hospital
Norway

Den 29.04.13 13:15, skrev Stephane:

To view this discussion on the web visit https://groups.google.com/d/msg/icy-software/-/2YDns-bhefAJ.

[Stephane]

Hi,

Generally that type of microscope generate multi series image (with different resolution) so even if Icy can't open the full resolution, you should be able to open a sub resolution of the image.
We are also developing a plugin which may be used to split very large images in tiles but again we are very dependant to what the Bio-Formats library is able to do so it could be limited in some way. Did you try to re open your image with the last version of Bio-Format ? you should have received an automatic update last friday.

Cheers,

- Stephane

[Curtis Rueden]

Hi Stephane & everyone,

> We are also developing a plugin which may be used to split very large

> images in tiles but again we are very dependant to what the

> Bio-Formats library is able to do so it could be limited in some way.

Bio-Formats provides an API for opening very large image planes in tiles:

    byte[] openBytes(int no, int x, int y, int w, int h)

    byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)

Any valid tile width and height should behave correctly, but for optimal performance you can ask for the data's ideal tile size using:

    int getOptimalTileWidth()

    int getOptimalTileHeight()

So hopefully it would not be too difficult for Icy to provide a "crop image on import" sort of feature -- and maybe eventually a tile-based image viewer. Please let us know if you have any trouble with it!

Regards,

Curtis

P.S. This week, the ImageJ2 team will be working on the underpinnings in ImgLib2 for a SCIFIO-driven CellImg with intelligent disk caching. Once this work is ready, and if Icy becomes capable of using ImgLib2 data structures at the interface level, you could potentially harness this feature for tile-based image support.

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[Stephane]

Hi Curtis,

Thanks for the information.
We are currently testing the following method to open image tile by tile:

   byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)

but it appears that all reader do not support it very well, we tested both on JPEG and NDPI reader and obtained errors in both case. Is there any way to know how much this method is supported ?

Glad to hear about the IJ2 work on smart image disk caching, i am impatient to see that in action :)

Cheers,

- Stephane